Genetic Drift, Not Life History or RNAi, Determine Long-Term Evolution of Transposable Elements

No evidence that sex and transposable elements drive genome size variation in evening primroses

(2015) J. Arvid Ågren et al.   EVOLUTION

No Accumulation of Transposable Elements in Asexual Arthropods

(2015) Jens Bast et al.   MOLECULAR BIOLOGY AND EVOLUTION

The plant parasite Pratylenchus coffeaecarries a minimal nematode genome

(2015) Mark Burke et al.   NEMATOLOGY

Ancient and Novel Small RNA Pathways Compensate for the Loss of piRNAs in Multiple Independent Nematode Lineages

(2015) Peter Sarkies et al.   PLOS BIOLOGY

ReproPhylo: An Environment for Reproducible Phylogenomics

(2015) Amir Szitenberg et al.   PLoS Computational Biology

Reproductive Mode and the Evolution of Genome Size and Structure in Caenorhabditis Nematodes

(2015) Janna L. Fierst et al.   PLoS Genetics

The Evolution of Selfing Is Accompanied by Reduced Efficacy of Selection and Purging of Deleterious Mutations

(2015) R. Arunkumar et al.   GENETICS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Mating system shifts and transposable element evolution in the plant genus Capsella

(2014) J Ågren et al.   BMC GENOMICS

Transposable Element Dynamics among Asymbiotic and Ectomycorrhizal Amanita Fungi

(2014) Jaqueline Hess et al.   Genome Biology and Evolution

The Relation between Recombination Rate and Patterns of Molecular Evolution and Variation in Drosophila melanogaster

(2014) José L. Campos et al.   MOLECULAR BIOLOGY AND EVOLUTION

“One code to find them all”: a perl tool to conveniently parse RepeatMasker output files

(2014) Marc Bailly-Bechet et al.   Mobile DNA

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Architecture and evolution of a minute plant genome

(2013) Enrique Ibarra-Laclette et al.   NATURE

SURFACE: detecting convergent evolution from comparative data by fitting Ornstein-Uhlenbeck models with stepwise Akaike Information Criterion

(2013) Travis Ingram et al.   Methods in Ecology and Evolution

Alu elements in primates are preferentially lost from areas of high GC content

(2013) Elizabeth HB Hellen et al.   PeerJ

Transposable Elements: An Abundant and Natural Source of Regulatory Sequences for Host Genes

(2012) Rita Rebollo et al.   Annual Review of Genetics

SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes

(2012) Elmar Pruesse et al.   BIOINFORMATICS

IS YOUR PHYLOGENY INFORMATIVE? MEASURING THE POWER OF COMPARATIVE METHODS

(2012) Carl Boettiger et al.   EVOLUTION

Molecular Evolution in Nonrecombining Regions of the Drosophila melanogaster Genome

(2012) José L. Campos et al.   Genome Biology and Evolution

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Function, Targets, and Evolution of Caenorhabditis elegans piRNAs

(2012) M. P. Bagijn et al.   SCIENCE

How does selfing affect the dynamics of selfish transposable elements?

(2012) Thibaud S Boutin et al.   Mobile DNA

The struggle for life of the genome's selfish architects

(2011) Aurélie Hua-Van et al.   Biology Direct

Repetitive Elements May Comprise Over Two-Thirds of the Human Genome

(2011) A. P. Jason de Koning et al.   PLoS Genetics

Crypton transposons: identification of new diverse families and ancient domestication events

(2011) Kenji K Kojima et al.   Mobile DNA

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

ETE: a python Environment for Tree Exploration

(2010) Jaime Huerta-Cepas et al.   BMC BIOINFORMATICS

Alternative splicing and evolution: diversification, exon definition and function

(2010) Hadas Keren et al.   NATURE REVIEWS GENETICS

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating

(2009) Nicolas Lartillot et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Epigenetic Reprogramming and Small RNA Silencing of Transposable Elements in Pollen

(2009) R. Keith Slotkin et al.   CELL

Transposable Elements and Factors Influencing their Success in Eukaryotes

(2009) E. J. Pritham   JOURNAL OF HEREDITY

The impact of retrotransposons on human genome evolution

(2009) Richard Cordaux et al.   NATURE REVIEWS GENETICS

A phylogenetic tree of nematodes based on about 1200 full-length small subunit ribosomal DNA sequences

(2009) Hanny van Megen et al.   NEMATOLOGY

The B73 Maize Genome: Complexity, Diversity, and Dynamics

(2009) P. S. Schnable et al.   SCIENCE

LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons

(2008) David Ellinghaus et al.   BMC BIOINFORMATICS

Endogenous RNA Interference Provides a Somatic Defense against Drosophila Transposons

(2008) Wei-Jen Chung et al.   CURRENT BIOLOGY

Population epigenetics

(2008) Eric J Richards   CURRENT OPINION IN GENETICS & DEVELOPMENT

Patterns of Molecular Evolution in Caenorhabditis Preclude Ancient Origins of Selfing

(2008) A. D. Cutter et al.   GENETICS

Chromodomains direct integration of retrotransposons to heterochromatin

(2008) X. Gao et al.   GENOME RESEARCH

Genomic Consequences of Outcrossing and Selfing in Plants

(2008) Stephen I. Wright et al.   INTERNATIONAL JOURNAL OF PLANT SCIENCES

Piwi and piRNAs Act Upstream of an Endogenous siRNA Pathway to Suppress Tc3 Transposon Mobility in the Caenorhabditis elegans Germline

(2008) Partha P. Das et al.   MOLECULAR CELL

Retrotransposon Tf1 Is Targeted to Pol II Promoters by Transcription Activators

(2008) Young-Eun Leem et al.   MOLECULAR CELL

Drosophila endogenous small RNAs bind to Argonaute 2 in somatic cells

(2008) Yoshinori Kawamura et al.   NATURE

An endogenous small interfering RNA pathway in Drosophila

(2008) Benjamin Czech et al.   NATURE

The Pristionchus pacificus genome provides a unique perspective on nematode lifestyle and parasitism

(2008) Christoph Dieterich et al.   NATURE GENETICS

The evolution of RNAi as a defence against viruses and transposable elements

(2008) D. J Obbard et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Endogenous siRNAs Derived from Transposons and mRNAs in Drosophila Somatic Cells

(2008) M. Ghildiyal et al.   SCIENCE

Phylogenetic Signal, Evolutionary Process, and Rate

(2008) Liam J. Revell et al.   SYSTEMATIC BIOLOGY